The Mare of Shadows
by killerpokeball97
Summary: AU One night, Twilight decided to test out a Spell with dark magic, this caused a shadow to form. The shadow is looking for revenge, but on who? Lemon later on in the series. AU Pre-Alicorn twilight and Pre- Discord reformation, and post-Season 3. WIP
1. It begins

Killer: hello everyone here's my first attempt at a my little pony fanfic tell me what you think of it ask questions if you want to

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><p><em>Chapter 1: The spell that started hell<em>

the scene opens up on Golden Oaks Library sometime during the night. Twilight was going over some books she borrowed from Princess Celestia, Her favorites involved pony genealogy, mythical spells, and Math. But this one book she was reading was about dark magic. Ever since she saw celestia do it then copied her, she's been wanting to study more about it. she didn't realize things were going to hell after reading this page.

"Necropasa terrolina argolinta colorupit shallow" Twilight read, "what an odd spell" she said unaware her horn glowed with dark magic which released a shadow which hid.

"I better get some sleep now, I can barely keep my eyes open" Twilight said with a yawn, she'll know more in the morning. she was unaware of the Hell she just summoned.

the shadow disappeared into the darkness. it had big plans in store.

_the next day..._

Twilight opened her eyes then yawned, she had the weirdest dream, she was standing alone in darkness. she saw the eyes of those she defeated before, only they looked more menacing. especially Nightmare Moon, she had the most twisted grin of them all. soon they all chanted to her, "one of us" over and over again.

"uggh, i feels like I was hit in the head by the train." groaned Twilight as she got out of bed and headed to her shower.

she began to wash herself...well she tried too but or some reason, the ONLY thing she was able to think about was Princess Celestia. she didn't feel like washing anymore so he dried herself of and walked out of the library, spike was still asleep. she headed to Sweet Apple Acres,she figured she could go for a round of apple cider. When she got to the farm however...

"WHAT HAPPENED HERE?" she shouted, the barn was dismantled, the trees were wilted, Granny smith and Big machintosh had their heads down in depression.

"excuse me Granny smith?" said twilight.

"Wahh, who that? AH DON'T HAVE ANEH BITS!" she shouted before realizing it was only twilight, "oh mah mistaike twilaught" she said.

"we dun't know wha happened, we jus woke up and applejack wus gone" Big Mac said to twilight.

"But what about the farm?" asked Twilight

"We'll repair it" said Big Mac

"without applejack?" asked twilight

"eeeyup, we atleast ahave tuh tra" said Big mac

"I supposed if you don't need any help" sighed twilight, maybe Applejack was over at Sugar cube corner helping Pinkie Pie.

But she got the same response from the Cakes, all the baked goods were destroyed as well, so Mr. and Mrs. Cake had to make new ones. Twilight knocked on Carousel Boutique and waited, when nopony answered the door, she saw all of Rarity's clothes were torn apart, especially her lingerie Cabinet. Sweetie belle wasn't home either, chances were that she was either at her fathers house, hasn't woken up yet, or with her friends. Twilight shut the door then headed to Fluttershy's cottage, she opened the door to see a crying angel bunny.

"angel? have you seen Fluttershy?" asked Twilight.

Angel bunny nodded as he did a charades bit, Twilight had trouble translating it but she managed to.

"you're saying that a shadow came and snatched her up?" asked Twilight, Angel nodded.

"this is serious, first Applejack is missing, then Pinkie Pie, then Rainbow Dash, then Rarity, and NOW fluttershy. what's going on here?" asked twilight before angel handed her a note.

"huh? what's this?" she asked before she read over the note.

"Dear Twilight Sparkle, I shall thank you for releasing me from my prison, come to the castle in Canterlot for a little surprise. I also have your friends held hostage - ? P.S I am everywhere, yet I remain in one place." Twilight finished reading. she gasped before running out the door leaving angel behind.

Twilight got on the train as fast as she could, she headed to Canterlot hoping her friends were all right.

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><p>Note 1: HI HO! I'm back everypony, I decided to update chapter 1 of this fanfic. I'll be updating periodically from now on, usually depending if I have anythingelse to do.<p>

Note 2: as the summary says, this is an AU before the Discord reformation and before alicorn twilight but before season 3 finished.

Note 3: to those who commented on the old chapter, I hope you like the improvements I made.


	2. Confronted by Darkness

Killer: Update time for this chapter!

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><p><em>Chapter 2: Confronted by Darkness <em>

_Twilight's POV_

as I rode the train to Canterlot, the train hit a road block so it will taken them a while to fix it. The roadblock itself was a giant vine blocking the way. It reminded me about some of those tree vines I saw in the everfree forest. I decided to come out of the train and see if there was anything I could do to help.

"Pardon me sirs" I told the two stallions who were trying to dig out the vines.

"We are sorry miss, this vine is blocking out way. It'll take a while in order to actually remove it, but if you can help us, it would REALLY be appreciated." said the stallion conductor.

I nodded and faced the vines, this shouldn't be too hard and take too long right?

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><p><em>Applejacks POV<em>

I woke up with a splitting headache, I think I drank too much apple cider yesterday. I looked around and I realized me and the others were in the throne room of Canterlot. Apparently I was the first to wake up because the others were still out cold. I froze up as I looked at the throne, the princess was inside of some Dark cocoon and there was some shadow pony sitting on the throne.

"minutes, hours, years, time has gone hasn't it?" said the shadow pony. I couldn't make out any details at all, I only see a body of a mare shrouded in darkness, but that was it.

"wha in tarnation is goin on!" I demanded an answer to the shadow pony. Apparently she didn't notice that I had woken up.

"Honesty...you make me sick." said the Shadow pony.

"Honesty? you mean mah Element?" I asked confused.

"don't act like you don't know what I am Honesty. It's because of YOU, that I became who I am today. I've been imprisoned for years because of YOU." said the shadow pony. I don't know how to respond, she's acting like I'm somepony she knows, does it have something to do with my element?

"ah'm sorry but, have we met?" I asked confused.

"Don't think you don't remember me honesty. We used to be friends, you introduced me to your friends, I thought I could trust you, but what did you do? you went out an betrayed me!" said the shadow pony angrily as a strike of lightning just missed me.

"Ah honestly have no idea wha ya'll talkin 'bout" I said trying to describe to her I'm not who she thinks I am. What was she talking about?

"Grrr, Fine if you won't respond, I'll show you what I went through-" before the shadow mare could finish I heard the door to the throne room burst open. inside ran Twilight.

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><p><em>Twilight's POV<em>

I made it to the throne room in Canterlot just in time. I was surprised and shocked from what I saw. I noticed Applejack was the only one who seemed awake, the others looked like they were still sleeping. Another thing I noticed was that Celestia was unconscious inside of a cocoon made from shadows.

"Applejack!" I shouted as I ran up to her.

"Twilaught, ah'm lucky ya'll got 'ere" she said to me.

"I was lucky enough to make it just in time, I was on the train when we hit a roadblock, luckily I managed to destroy it and allow the train to continue. after I made it to Canterlot I teleported most of the way to the castle." I said Happily.

"twilaught, ah need ya tuh talk some sense into this pony, she's actin lak she knows us" applejack told me. I turned to the shadow pony and was about to say something when she started telling me something I couldn't believe.

"Magic, you really were my only friend right next to Honesty. But I still HAVEN'T forgiven you for what you did to me!" shouted the shadow pony.

"what did I do to you?" I asked confused. My history book on the Elements of Harmony never told me about a shadow pony. Could I have overlooked something?

"You used your magic to destroy my body, you crushed my spirit, you never felt sorry for me. It's because of YOU and HONESTY that I have become what I became, it's because of YOU that I was banished." the shadow pony said, for some reason it felt like Daggers were being sliced through my heart.

"Destroy your body? Crush your spirit? We don't know what you are talking about!" I shouted.

"Boulderdash!" the shadow pony shouted, it turned to Celestia who started to regain consciousness.

"YOU!" shouted Celestia who tried to break out of the cocoon.

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><p>Note: for an update, it's pretty nice<p>

Note 2: those who haven't seen the original draft, it was abit less dramatic than this draft.

Note 3: I will continue to update.


	3. The Dark Queen rises

Killer: Since I didn't get the desired number of votes I named the mare myself

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><p><em>Chapter 3: the Queen of Darkness rises<em>

Celestia's POV

I have no idea what happened, one minute I was just sleeping then the next I wake up in this chrysalis, I looked around and saw Twilights friends aside from Applejack all apparently still asleep. I wanted to say something but at the moment, I couldn't. I saw the doors burst open and saw my faithful student run in and stop by her friends. I couldn't make out what they were saying.

"TWILIGHT!" I shouted through the chrysalis, but the shout didn't make it through. I then a heard a voice beside me, No...it couldn't be...NOT HER!

"YOU!" I shouted after I turned to the Shadow pony who was sitting on my throne.

"ahhh so nice to see you are awake madam Celestia." said the shadow pony as I tried to use my magic to burst out of the chrysalis

"YOU! WHY ARE YOU BACK!? YOU WERE BANISHED!" I shouted in the royal canterlot voice.

"ahh, so the Princess really DOES recognize me. Very well, I might as will reveal my Identity before I go one with my plan." said the shadow pony before her body started getting color. She had a Pinkish white coat, with a black mane with a midnight blue steak down it, she was about Twilight's height. the Pony opened her eyes, the pupils were Slit-like just like my sister when she turned into Nightmare Moon. she looked ALMOST EXACTLY like Twilight.

"that's much better" said the Pony. I only growled, WHY is she here? WHY!?

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><p>Twilight's POV<p>

I watched the conversation between the Princess and the shadow mare, my eyes widened when I saw the pony gain some color, what was even weirder was, the pony looked ALMOST like me, right down to the streak in the hair.

"PRINCESS!" I shouted to Celestia as I ran up to her. The used-to-be shadow mare made no attempt to stop me.

"Twilight, you HAVE to get out of here!" said Celestia to me.

"But princess! who is this pony!? and WHY does she look like me?!" I was practically starting to beg an explanation at this point.

"oh Magic, how nice to FINALLY open my eyes and see you, you STILL have the look of betrayal I saw when I was banished" said the mare

"Shut it! who are you anyway?!" I shouted angrily.

"fine, if you can't remember me magic, allow me to give you a glimpse of the past." said the mare as her eyes turned blue, I stared before I felt myself going into a trance, it feels like that time I looked through King Sombra's door in the crystal empire.

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><p><em>after the vision<em>

Twilight's POV

I had tears in my eyes, I couldn't believe what I saw. WHY would they do that to her?! WHY didn't they forgive her!?

"you see Magic, that's the reason why I'm, going to have revenge on you and the rest of the ponies! Your body could be of use as well" said the mare. Before I could respond I was held up in the air by dark magic.

"ALL SHOW TREMBLE AT THE MENTION OF MY NAME, THE QUEEN OF DARKNESS, DARKLIGHT ECLIPSE!" shouted the mare as she floated up to my body then stuck her hoof inside. I didn't have time to react before she suddenly stuck her other hoof in, then her head, then her body.

"GAAAAAAAAAHHHHHHHHHHHH!" I shouted as I felt the mare's body merge with my own. I started to grow paterns over my body, I felt my mane change it felt like it was flowing without wind. My coat started to change color, it went from Lavender to periwinkle. A sharp pain coursed through my skull as I felt my mind being assimilated with he mare. My pupils turned to slits as my mane and tail's Pinkish streak turned to blue.

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><p>Applejacks POV<p>

I watched Twilight run toward Celestia, I wanted to run as well but my hooves wouldn't move no matter how hard I tried. I saw Twilight talk with the mare before she went into a trance. After she got out of the trance, the next thing that happened made me wide eyed, Twilight was lifted into the air by dark magic. My jaw dropped when I saw the mare enter Twilight's body, I stared in horror at Twilight's transformation. Celestia was trying with all her might to break out of the cocoon but it was all in vain.

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><p><em>Twilight's mind<em>

Twilight was floating in a void of nothingness, her world, it all came crashing down on her the moment the Dark queen started to take over her body, originally this mind was full of books and her friends.

Darklight Eclipse suddenly grabbed hold of her and forced her into darkness, the void turned dark, her eyes turned to the same color as the mares which was an icey blue.

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><p><em>back in the throne room AFTER the transformation<em>

"I...live!" shouted the new Mare

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><p>Note: Update for the original chapter.<p>

Note 2: Changed the name from Nightmare Light to Darklight Eclipse.

Note 3: have you notices that in alot o my stories I ALWAYS seem to provide 3 notes at the end of each chapter?


	4. Twilight Eclipse and Honesty lies

Killer: Hello everypony, last update for the original chapters.

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><p><em>Chapter 4: Twilight Eclipse and Honesty's lie<em>

Twilight Eclipse floated to the ground, she was Twilight but with a changed coat, she looked Elegant in appearence almost like a queen.

"ahhh, that is much better" said Twilight Eclipse admiring her new form.

"Twilaught! wha happened tah you?!" Shouted Applejack.

"Twilight? oh I'm sorry, you're prescious twilight is part of me now, Magic is back to my side now, she FINALLY saw the error of her ways. I'm no longer just Darklight Eclipse, I am now TWILIGHT ECLIPSE!" she laughed evilly which turned into a cackle.

"now, What to do with you" said Twilight Eclipse to Celestia.

"You AREN'T going to get away with this!" shouted Celestia, if this cocoon wasn't stopping her magic and if it didn't weaken her, she would have busted out by now.

"I'm afraid I can, have, and did" said Twilight Eclipse

"now, for YOUR punishment for helping to banish me, I shall take YOUR alicorn power for my own" cackled Twilight Eclipse as she pointed her horn at Celestia then fired a dark beam. Celestia couldn't move as she felt her power get drained, she felt sleepy, she didn't have much energy.

"that feel MUCH better, with the power of Celestia herself, I am unstoppable!" Twilight Eclipse cackled once again.

"now, what to do with you and the others honesty" said Twilight Eclipse as she used her magic to lift up the rest of the mane cast.

"Those still sleeping, I KNOW you can hear me, soon you ALL will feel the torment I had to go through, and I will enjoy EVERY second of it" said Twilight Eclipse with an evil grin

"I'll start with YOU first honesty" said Twilight Eclipse before sending the mane 5 all across Equestria in separate directions. the only way they'll be able to find each other again is hope.

Twilight Eclipse was Clueless of one thing, 5 spirits flew away from the castle without her noticing.

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><p>Applejack woke up in a tree in a desert land she recognized the land as Appleloosa.<p>

"Thank Goodness ah'm in a place ah can remember, ah have to fahnd the outhers tah help saive twilaught!" she got down from the tree then headed into town but saw it was Deserted nopony was around.

"Hello! Anypony 'round 'ere? Braeburn! Sheiff Silver star! ...Little Strong Heart?!" She called out but recieved no answer.

Applejack saw a pony run out of the corner of her eye this pony looked frightened, "Ehy! Wait up!" she shouted after him and started to trot But he only kept running as if fleeing from Something.

"LEAVE ME ALONE! LEAVE ME ALONE YOU MONSTER!" he Shouted while running. Applejack was taken back from what he Shouted She looked around but she saw nothing.

"This better not be a Prank somepony is playin on me" she walked toward the House which she recongized as her cousin Braeburns house. She ran up to it and knocked on the Door.

"Braeburn ya'll there? it's me Applejack!" she Called but she didn't get an answer so she knocked again.

"Braeburn! are you in there?" again she recieved no response. "Whah is everypony hidin?" she asked herself as she walked around the town looking at the cowering Ponies in their homes some even fainted after looking at Applejack through their Windows.

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><p><em>Sheriffs office<em>

"Sheriff What Happened to Applejack? She looks completely different I'm too frightened to think about it!" He said in a Panic

"Now Braeburn We don't know wha happened tah her, But we have tah keep oua distance from her, just one look could chill a pony to the bone." the Sheriff Told him.

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><p><em>Outside<em>

Applejack just kept walking around town looking at the buildings and the ponies inside of them, some froze with fear after she Looked at them.

'Wha is everypony actin lak they are afraid of me? it doesn't make a likin scence!' she shouted in her Head. She stopped at the Salt Block and opened the door but nopony was inside. she closed the door and the Ponies inside that were hiding came out making sure Applejack wasn't at the door.

"Sheiff ah'm Going to try to talk with her" said Braeburn before he could walk out the Sheriff stopped him

"Wait! ya'll don't know if she's safe!" Braeburn turned around with a confident look.

"Dun worry Sheriff Ah'lll be okay" and with that Braeburn Walked out of the Sheriff's Office toward Applejack with a Twisted smile that was unlike him.

Applejack saw her cousin walk toward her She was surprised and happy to see him then ran up to Him, BUT something was Different about him. All Braeburn saw running infront of him was a half alive and half dead pony that Looked EXACTLY like Applejack.

"Braeburn! am ah glad to see you what's wrong with everypony in th-" she was stopped at the sound of a Gun Being loaded. Braeburn Loaded a Shotgun and Pointed it at Applejack

"Get the buck out of Town you zompony Freak" he said Pointing the Gun at Applejack.

Applejack was completely surprised by the outcome and tackled Braeburn to Stop Him, But Braeburn was quick to wrestle applejack off then run toward his Gun.

"Braeburn! What's Gotten into you!?" she Shouted as he fired he gave her a warning shot and dared her to Come Closer.

"I said GET OUT OF TOWN YOU ZOMPONY FREAK!" he shouted then Fired a Bullet which Applejack Narrowley Dodged. she was Heart Broken about how her relative was treating her she had no choice but to run away. Braeburn watched her run and for some reason he felt completely sad about what he did.

"What have I Done...?" he asked Himself in shock before dropping his gun and falling face first onto the dirt.

Applejack was running she didn't know where or why she was Running away from the town, but she was Crying as she did. she Never felt so sad in all her Life.

"Wha was Everypony scared of me? Why did Braeburn call meh ah Zompony freak? Why did he almost shoot me?" She kept asking herself these questions until she came to a lake somewhere in the Desert, not wanting to question why, she went to it, then Dipped her Hooves in then Brought them to her Face to calm herself down. She Looked Down at her reflection and was horrified because, Staring back at her was a pony in the same coat color, but Some parts of her body were Dead and Rotting, and a Skull replaced her Face and the only things in her eye sockets were Blue Fires.

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><p><em>Canterlot castle<em>

Twilight Eclipse was watching through a magic mirror at Applejack her plan for Honesty was working, thanks to her Magic she made everypony in Appleloosa see Applejack as a necropony and forced her out of town, she smiled sadistically.

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><p><em>Desert<em>

Applejack's mind felt like it was breaking, because she actually felt her face, she felt a skull. She Hugged herself in fear but felt bone where parts of her flesh should be. Because of Twilight Eclipses power, Applejack no longer felt as honest as before. Applejack Sobbed for a while saying she's not a zompony, but because of the Dark Magic of Twilight Eclipse, Applejacks mind says it's the truth when it really isn't, thus Leaving Applejack to feel dejected from society.

"WHY? WHY IS THIS HAPPENING?! I"M A PONY NOT A ZOMPONY! AH'M NOT!" She Ran off in a Random Direction crying to herself on what she is, she didn't know whre she was going, nor did she care.

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><p><em>Canterlot Castle<em>

Twilight Eclipse smiled sadistically at applejack through the mirror, THIS is the pain she felt from the other elements, THIS is the reason why she became this way.

"How does it feel to be dejected from everypony? Does it feel good? HMM?" she cackled at the mirror.

"I have plans for YOUR friends as well" she said before looking out the window.

"I must really need to lower the sun in a few minutes, but until then." she said before turning to the caged Celestia.

"you will stay asleep, perhaps forever" cackled Twilight Eclipse.

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><p>Note: the Original draft was abit different<p>

Note 2: Whoever get's what I'm going to do in the Next chapters for the beggining and Pointing out the reference will get a cookie. what kind? chocolate chip.

Note 3: those 5 spirits are the rest of the personified Elements of Harmony, where will they end up? find out later.

Note 4: There's FINALLY a note 4.


	5. Intermission

_Attention followers and ponies and people who view this. This story will be getting moved to later an will be deleated from this website._

_I am happy to see how everypony was, my story, sure it hit a few snags, but I resolved most of it. so to anypony else who will read this, this story is going to be abit better than it was on here._

_So once again, thank you for reading._


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